Getting Started with VnmrJ Liquids NMR

1 Getting Started withVnmrJ LiquidsNMRV arian NMR Spectrometer Systemswith VnmrJ SoftwarePub. No. 01-999150-00, Rev. C0503 Getting Startedwith VnmrJLiquids NMRV arian NMR Spectrometer Systemswith VnmrJ SoftwarePub. No. 01-999150-00, Rev. C0503 Getting Started with VnmrJ Liquids NMRV arian NMR Spectrometer Systemswith VnmrJ SoftwarePub. No. 01-999150-00, Rev. C0503 Revision history:A0802 Beta test releaseA1002 Updated for VnmrJ of manual:Varian NMR spectrometer systems with VnmrJ contributors: Bayard Fetler, Maj Hedehus, Dan Iverson, He Liu, Chris Price,Evan WilliamsTechnical writer: Everett Schreiber, Dan SteeleTechnical Editor: Dan SteeleCopyright 2003by Varian, Hansen Way, Palo Alto, California 943041-800-356-4437 rights reserved. Printed in the United information in this document has been carefully checked and is believed to beentirely reliable. However, no responsibility is assumed for inaccuracies.

2 Statements inthis document are not intended to create any warranty, expressed or and performance characteristics of the software described in this manualcan be changed at any time without notice. Varian reserves the right to make changes inany products herein to improve reliability, function, or design. Varian does not assumeany liability arising out of the application or use of any product or circuit describedherein; neither does it convey any license under its patent rights nor the rights of in this document does not imply that any particular feature is standard on ,MERCURY plus,MERCURY-VX,MERCURY,Gemini,GEMINI 2000, UNITY plus,UNITY, VXR, XL, VNMR, VnmrS, VnmrX, VnmrI, VnmrV, VnmrSGI, MAGICAL II,AutoLock, AutoShim, AutoPhase, limNET, ASM, and SMS are registered trademarks ortrademarks of Varian, Inc. Sun, Solaris, CDE, Suninstall, Ultra, SPARC, SPARC station,SunCD, and NFS are registered trademarks or trademarks of Sun Microsystems, Inc.

3 AndSPARC International. Oxford is a registered trademark of Oxford Instruments is a registered trademark of Xerox Corporation. VxWORKS and VxWORKSPOWERED are registered trademarks of WindRiver Inc. Other product names in thisdocument are registered trademarks or trademarks of their respective C0503 VnmrJ : Gettiing Started with Liquids NMR4 Table of ContentsChapter Road Map .. Bar .. 11 Hiding and Showing the Menu Bar .. Bar .. 22 Hiding and Showing the Tool Bar .. Pen .. Controls Bar .. Function Bar .. Canvas .. Controls .. Panels .. Bar .. 25 Trash Can .. 25 Temp Button .. 26 Spin Button .. 26 Lock Button .. 26 Probe .. 27 Seeing Acquisition Status Details .. 27 Seeing Remaining Experiment Time .. 27 Seeing a History of Acquisition Messages .. 28 Seeing a History of All Messages.

4 28 Message Display .. 28 Hiding and Showing the Hardware Bar .. 28 Chapter .. Interface Elements .. 31 Locator Statements and Menu .. 31 Navigation in the Locator .. 32 Locator Groups .. 32 Attributes .. the Locator .. 33 Searches .. 33 Dragging and Dropping Items from the Locator .. 33 Editing File Names from the Locator .. Statements .. 34 Sort Workspaces .. 34 Sort NMR Data .. 34 Sort NMR Parameter Files .. 35 Sort Shimsets .. 35 Sort Command Macros .. 35 Chapter 1D and 2D Experiments .. VnmrJ .. for Running an NMR Experiment .. 37 Table of Contents5 VnmrJ : Gettiing Started with Liquids NMR01-999150-00 the Sample and Loading a Probe File .. 38 Ejecting and Inserting a Sample .. 38 Loading a Probe File .. , Setting Spinning Speed, and Adjusting Homogeneity .. 39 Setting Spinner Speed.

5 39 Finding Z0 and Establishing Lock .. 39 Adjusting the Field , Loading and Setting Up a 1D Experiment .. 41 Menu Method .. 41 Locator Method .. 42 Selecting a Solvent .. 42 Naming a Sample (optional) .. 43 Setting Up Experimental Parameters .. 43 Setting the Temperature for VT Control (optional) .. 43 Setting Up Auto Process and Plot .. 43 Setting Up Acquisition and Post Acquisition Actions .. a Spectrum .. 44 Menu Method .. 45 Parameter Panel Method .. and Displaying 1D NMR Data .. 45 Parameter Panel Method .. 45 Display Bar Icons .. the NMR Data (optional) .. 46 Menu Method .. 47 Parameter Panel Method .. the Spectrum (optional) .. an Experiment .. , Loading, and Setting Up a 2D Experiment .. 48 Choosing and Loading a 2D Experiment .. 48 Naming the Sample, Selecting the Solvent, Setting VT, and Post Acquisition Events49 Setting Up Experimental Parameters.

6 49 Acquiring a Spectrum .. 49 Processing 2D NMR Data .. 49 Saving the 2D Data .. 49 Plotting the 2D Spectrum .. 49 Chapter , Data Saving, Template Editor, and Shim Buttons New Parameters and Environment Variables .. Automatic Data Saving .. 50 System Settings .. 50 Current Experiment .. 51 Saving Selected FIDs .. the Template Editor .. 51 Hints When Viewing a 52 Commonly Used Panel Items .. 52 Attributes of Commonly Used Items .. 52 Hints When Editing a Panel .. the Shim Buttons .. 53 Table of Contents01-999150-00 C0503 VnmrJ : Gettiing Started with Liquids NMR6 Chapter and ECC Utilities .. Requirements .. the ECC Software .. 56 Setting Up the System for ECC .. 56 Determining the ECC Parameters .. 57 Updating the Probe File and Enabling ECC .. ECC into Each User Account.

7 60 Enabling ECC for Each User Account .. the Enhanced DSP .. Gradients .. Tests .. 64 List of Figures7 VnmrJ : Gettiing Started with Liquids NMR01-999150-00 C0503 List of FiguresFigure Interface (for Experiments) .. 10 Figure Parameter Window .. 12 Figure Tool .. 14 Figure Designer .. 14 Figure Settings Window .. 15 Figure Create New Parameters Window .. 16 Figure Data Setup Window .. 17 Figure Devices Window .. 17 Figure Options Window .. 18 Figure Dialog Window .. 18 Figure Custom Locator Statement Window .. 19 Figure Custom Locator Statement Window .. 19 Figure Editor .. 20 Figure Program .. 21 Figure Panel .. 21 Figure Canvas .. 24 Figure Panel Buttons .. 24 Figure Panel Tabs .. 25 Figure Can Mode .. 26 Figure Window .. 27 Figure Status Window.

8 27 Figure Statement .. 31 Figure Groups Menu .. 32 Figure Locator Statement .. 35 Figure in CDE Tool Bar .. 36 Figure Panel .. 38 Figure Panel .. 39 Figure Lock .. 39 Figure Panel .. 40 Figure Options .. 40 Figure Panel .. 41 Figure Accessed from the Menu Bar .. 42 Figure an Experiment from the Locator .. 42 Figure Panel - Default Tab .. 43 Figure when done Button .. 43 Figure Panel .. 44 Figure Actions Panel .. 44 Figure H1 Panel .. 45 Figure Panel .. 45 Figure Icons Bar .. 46 Figure Data Setup Window .. 47 Figure the Spectrum .. 47 Figure Experiments Accessed from the Menu Bar .. 48 List of Figures01-999150-00 C0503 VnmrJ : Gettiing Started with Liquids NMR8 Figure Settings Window .. 51 Figure Editor .. 51 Figure Tab - Acquisition panel .. 58 Figure Tab - ECC panel.

9 58 Figure with No Eddy Current Compensation .. 59 Figure Fitting of the Data .. 59 List of Tables9 VnmrJ : Gettiing Started with Liquids NMR01-999150-00 C0503 List of TablesTa b le 1 .List of Commonly Used Items in a Panel .. 52Ta b le 2 .Attributes of Commonly Used Items .. 52Ta b le 3 .ECC Parameter and Ranges .. 5701-999150-00 C0503 VnmrJ : Gettiing Started with Liquids NMR10 Chapter Road MapThe VnmrJ interface for Liquids experiments is shown inFigure 1. The interface contains10 interaction areas. This chapter describes each of those areas. , Menu Bar, on page 11 , Tool Bar, on page 22 , Locator, on page 22 , Holding Pen, on page 23 , Graphics Controls Bar, on page 23 , Advanced Function Bar, on page 23 , Graphics Canvas, on page 24 , Action Controls, on page 24 , Parameter Panels, on page 25 , Hardware Bar, on page 25 Figure Interface (for Experiments)1.

10 Menu bar2. Tool bar3. Locator6. Advanced function window7. Graphics canvas8. Action controls9. Parameter panels10. Hardware bar4. Holding pen5. GraphiccontrolsChapter 1. VnmrJ Road Map11 VnmrJ : Gettiing Started with Liquids NMR01-999150-00 Menu BarThe menu bar sits along the top of the interface. Its function is twofold. The first function of the menu bar is to give you, as a new user, access to operationsneeded to acquire, process, and plot a spectrum. As you continue to use the interfaceand become more expert at using VnmrJ , you might have less use for the menu bar. The second function of the menu bar is to provide access to little-used features, settingpreferences, and other things that are rarely done and can be found in the Utilities, Edit,and Help following sections describe the options in the main menu contains a list of available pulse menu contains a list of available menu enables you to perform the following acquisition-related menu choice opens the Array Parameter tool shown inFigure top panel in the window is a table of currently arrayed parameters.